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Forum: Bioinformatics 05-29-2019, 08:14 PM
Replies: 4
Views: 483
Posted By questor2010
You should be able to use bcftools itself to...

You should be able to use bcftools itself to index the file. Just use "bcftools index 722g.990.SNP.INDEL.chrAll.vcf.gz"
Forum: Bioinformatics 05-06-2019, 10:39 AM
Replies: 12
Views: 973
Posted By questor2010
The -o switch specifies the output file name, the...

The -o switch specifies the output file name, the -O switch specifies the format:

-O, --output-type <b|u|z|v> b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF...
Forum: Bioinformatics 05-01-2019, 10:51 AM
Replies: 12
Views: 973
Posted By questor2010
Ouch. Yes - that's the problem. I hope you have...

Ouch. Yes - that's the problem. I hope you have another copy readily available. The index file warnings are often caused by file transfers. They transfer first for large files and then have an older...
Forum: Bioinformatics 05-01-2019, 09:35 AM
Replies: 12
Views: 973
Posted By questor2010
Sure - here's an example: bcftools view -f...

Sure - here's an example:

bcftools view -f PASS --threads 8 -T target.bed -o gnomad.genomes.r2.1.sites.target.vcf.gz -O z gnomad.genomes.r2.1.sites.vcf.bgz

In this case, I'm using a bed file,...
Forum: Bioinformatics 04-30-2019, 07:53 PM
Replies: 12
Views: 973
Posted By questor2010
Note that for very large vcf files, using -t/-T...

Note that for very large vcf files, using -t/-T instead of -r/-R is going to be much faster. And use the --threads option, that will help as well.
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